cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/FloraMalesianaVol13Activator.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.app.eflora;
  11
  12 import java.net.URI;
  13 import java.util.HashSet;
  14 import java.util.List;
  15 import java.util.Set;
  16 import java.util.UUID;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.transaction.TransactionStatus;
  20
  21 import eu.etaxonomy.cdm.api.service.ITermService;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  26 import eu.etaxonomy.cdm.io.common.events.IIoObserver;
  27 import eu.etaxonomy.cdm.io.common.events.LoggingIoObserver;
  28 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  29 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  30 import eu.etaxonomy.cdm.io.eflora.floraMalesiana.FloraMalesianaTransformer;
  31 import eu.etaxonomy.cdm.io.markup.MarkupImportConfigurator;
  32 import eu.etaxonomy.cdm.model.description.Feature;
  33 import eu.etaxonomy.cdm.model.description.FeatureNode;
  34 import eu.etaxonomy.cdm.model.description.FeatureTree;
  35 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  36 import eu.etaxonomy.cdm.model.reference.Reference;
  37 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  38
  39 /**
  40  * @author a.mueller
  41  * @created 20.06.2008
  42  * @version 1.0
  43  */
  44 public class FloraMalesianaVol13Activator {
  45         private static final Logger logger = Logger.getLogger(FloraMalesianaVol13Activator.class);
  46
  47         //database validation status (create, update, validate ...)
  48         static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  49         static final URI fmSource13_small = EfloraSources.fm_13_small_families();
  50         static final URI fmSource13_large = EfloraSources.fm_13_large_families();
  51         static final URI fmSource12 = EfloraSources.fm_12();
  52         static final URI fmSource2_2 = EfloraSources.fm_2_2();
  53
  54
  55
  56 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3();
  57 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_preview();
  58 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_malesiana_production();
  59         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  60 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
  61 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  62
  63         private boolean includeVol13_small = false;
  64         private boolean includeVol13_large = false;
  65         private boolean includeVol12 = false;
  66         private boolean includeVol2_2 = true;
  67
  68         private boolean h2ForCheck = true;
  69
  70
  71         //feature tree uuid
  72         public static final UUID featureTreeUuid = UUID.fromString("168df0c6-6429-484c-b26f-ded1f7e44bd9");
  73
  74         //classification
  75         static final UUID classificationUuid = UUID.fromString("ca4e4bcb-a1d1-4124-a358-a3d3c41dd450");
  76
  77         //check - import
  78         static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  79
  80         static boolean doPrintKeys = false;
  81
  82         //taxa
  83         static final boolean doTaxa = true;
  84
  85
  86         private boolean replaceStandardKeyTitles = false;
  87
  88         private IIoObserver observer = new LoggingIoObserver();
  89         private Set<IIoObserver> observerList = new HashSet<IIoObserver>();
  90
  91
  92         private void doImport(ICdmDataSource cdmDestination){
  93                 observerList.add(observer);
  94                 if (h2ForCheck && cdmDestination.getDatabaseType().equals(CdmDestinations.localH2().getDatabaseType())){
  95                         check = CHECK.CHECK_ONLY;
  96                 }
  97
  98                 //make Source
  99                 URI source = fmSource13_small;
 100                 MarkupImportConfigurator markupConfig= MarkupImportConfigurator.NewInstance(source, cdmDestination);
 101                 markupConfig.setClassificationUuid(classificationUuid);
 102                 markupConfig.setDoTaxa(doTaxa);
 103                 markupConfig.setCheck(check);
 104                 markupConfig.setDoPrintKeys(doPrintKeys);
 105                 markupConfig.setDbSchemaValidation(hbm2dll);
 106                 markupConfig.setObservers(observerList);
 107                 markupConfig.setReplaceStandardKeyTitles(replaceStandardKeyTitles);
 108
 109
 110                 markupConfig.setSourceReference(getSourceReference("Flora Malesiana - Vol. 13"));
 111
 112                 CdmDefaultImport<MarkupImportConfigurator> myImport = new CdmDefaultImport<MarkupImportConfigurator>();
 113
 114                 //Vol13_2
 115                 if (includeVol13_large){
 116                         System.out.println("\nStart import from ("+ fmSource13_large.toString() + ") ...");
 117                         source = fmSource13_large;
 118                         markupConfig.setSource(source);
 119                         myImport.invoke(markupConfig);
 120                         System.out.println("End import from ("+ fmSource13_large.toString() + ")...");
 121                 }
 122
 123                 //Vol13_1
 124                 if (includeVol13_small){
 125                         System.out.println("\nStart import from ("+ fmSource13_small.toString() + ") ...");
 126                         source = fmSource13_small;
 127                         markupConfig.setSource(source);
 128                         myImport.invoke(markupConfig);
 129                         System.out.println("End import from ("+ fmSource13_small.toString() + ")...");
 130                 }
 131
 132                 //Vol12
 133                 if (includeVol12){
 134                         source = fmSource12;
 135                         System.out.println("\nStart import from ("+ source.toString() + ") ...");
 136                         markupConfig.setSource(source);
 137                         myImport.invoke(markupConfig);
 138                         System.out.println("End import from ("+ source.toString() + ")...");
 139                 }
 140                 //Vol_2_2
 141                 if (includeVol2_2){
 142                         source = fmSource2_2;
 143                         System.out.println("\nStart import from ("+ source.toString() + ") ...");
 144                         markupConfig.setSource(source);
 145                         myImport.invoke(markupConfig);
 146                         System.out.println("End import from ("+ source.toString() + ")...");
 147                 }
 148
 149
 150 //              makeGeoService();
 151
 152                 FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService());
 153                 myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);
 154
 155                 //check keys
 156                 if (doPrintKeys){
 157                         TransactionStatus tx = myImport.getCdmAppController().startTransaction();
 158                         List<PolytomousKey> keys = myImport.getCdmAppController().getPolytomousKeyService().list(PolytomousKey.class, null, null, null, null);
 159                         for(PolytomousKey key : keys){
 160                                 key.print(System.out);
 161                                 System.out.println();
 162                         }
 163                         myImport.getCdmAppController().commitTransaction(tx);
 164                 }
 165
 166         }
 167
 168         private Reference getSourceReference(String string) {
 169                 Reference result = ReferenceFactory.newGeneric();
 170                 result.setTitleCache(string);
 171                 return result;
 172         }
 173
 174         private FeatureTree makeFeatureNode(ITermService service){
 175                 FloraMalesianaTransformer transformer = new FloraMalesianaTransformer();
 176
 177                 FeatureTree result = FeatureTree.NewInstance(featureTreeUuid);
 178                 result.setTitleCache("Flora Malesiana Presentation Feature Tree");
 179                 FeatureNode root = result.getRoot();
 180                 FeatureNode newNode;
 181
 182                 newNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 183                 root.addChild(newNode);
 184
 185                 addFeataureNodesByStringList(descriptionFeatureList, newNode, transformer, service);
 186
 187                 addFeataureNodesByStringList(generellDescriptionsUpToAnatomyList, root, transformer, service);
 188                 newNode = FeatureNode.NewInstance(Feature.ANATOMY());
 189                 addFeataureNodesByStringList(anatomySubfeatureList, newNode, transformer, service);
 190
 191                 newNode = addFeataureNodesByStringList(generellDescriptionsFromAnatomyToPhytoChemoList, root, transformer, service);
 192                 addFeataureNodesByStringList(phytoChemoSubFeaturesList, newNode, transformer, service);
 193
 194                 newNode = addFeataureNodesByStringList(generellDescriptionsFromPhytoChemoList, root, transformer, service);
 195
 196
 197                 newNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
 198                 root.addChild(newNode);
 199
 200                 newNode = FeatureNode.NewInstance(Feature.ECOLOGY());
 201                 root.addChild(newNode);
 202                 addFeataureNodesByStringList(habitatEcologyList, root, transformer, service);
 203
 204                 newNode = FeatureNode.NewInstance(Feature.USES());
 205                 root.addChild(newNode);
 206
 207                 addFeataureNodesByStringList(chomosomesList, root, transformer, service);
 208
 209                 newNode = FeatureNode.NewInstance(Feature.CITATION());
 210                 root.addChild(newNode);
 211
 212                 return result;
 213         }
 214
 215         private static String [] chomosomesList = new String[]{
 216                 "Chromosomes",
 217         };
 218
 219
 220         private static String [] habitatEcologyList = new String[]{
 221                 "Habitat",
 222                 "Habitat & Ecology"
 223         };
 224
 225
 226         private static String [] generellDescriptionsUpToAnatomyList = new String[]{
 227                 "Fossils",
 228                 "Morphology and anatomy",
 229                 "Morphology",
 230                 "Vegetative morphology and anatomy",
 231         };
 232
 233
 234         private static String [] anatomySubfeatureList = new String[]{
 235                 "Leaf anatomy",
 236                 "Wood anatomy"
 237         };
 238
 239         private static String [] generellDescriptionsFromAnatomyToPhytoChemoList = new String[]{
 240                 "Flower morphology",
 241                 "Palynology",
 242                 "Pollination",
 243                 "Pollen morphology",
 244                 "embryology",
 245                 "cytology",
 246                 "Life cycle",
 247                 "Fruits and embryology",
 248                 "Dispersal",
 249                 "Chromosome numbers",
 250                 "Phytochemistry and Chemotaxonomy",
 251         };
 252
 253
 254         private static String [] phytoChemoSubFeaturesList = new String[]{
 255                 "Alkaloids",
 256                 "Iridoid glucosides",
 257                 "Leaf phenolics",
 258                 "Storage products of seeds",
 259                 "Aluminium",
 260                 "Chemotaxonomy",
 261         };
 262
 263
 264         private static String [] generellDescriptionsFromPhytoChemoList = new String[]{
 265                 "Phytochemistry",
 266                 "Taxonomy",
 267                 "history",
 268                 "cultivation",
 269                 "Notes"
 270         };
 271
 272
 273         private static String [] descriptionFeatureList = new String[]{
 274                 "lifeform",
 275                 "Bark",
 276                 //new
 277                 "wood",
 278                 "Indumentum",
 279                 "endophytic body",
 280                 "flowering buds",
 281                 "Branchlets",
 282                 "Branches",
 283                 "Branch",
 284                 "Flowering branchlets",
 285                 "Trees",
 286                 "Twigs",
 287                 "stem",
 288                 "Stems",
 289                 "stem leaves",
 290                 "Leaves",
 291                 "flower-bearing stems",
 292                 "Petiole",
 293                 "Petiolules",
 294                 "Leaflets",
 295                 "Thyrsus",
 296                 "Thyrses",
 297                 "Inflorescences",
 298                 "Inflorescence",
 299                 "Young inflorescences",
 300                 "Male inflorescences",
 301                 "Female inflorescences",
 302                 "Bracts",
 303                 "Pedicels",
 304                 "flowering buds",
 305                 "scales",
 306                 "Buds",
 307                 "Flowers",
 308                 "Flower",
 309                 "Flowering",
 310                 "Stigma",
 311                 "perianth",
 312                 "Sepals",
 313                 "Sepal",
 314                 "Outer Sepals",
 315                 "Axillary",
 316                 "cymes",
 317                 "Calyx",
 318                 "Petal",
 319                 "Petals",
 320                 "perigone",
 321                 "perigone lobes",
 322                 "perigone tube",
 323                 "Disc",
 324                 "corolla",
 325                 "Stamens",
 326                 "Staminodes",
 327                 "Ovary",
 328                 "Anthers",
 329                 "anther",
 330                 "Pistil",
 331                 "Pistillode",
 332                 "Ovules",
 333                 "androecium",
 334                 "gynoecium",
 335                 "Filaments",
 336                 "Style",
 337                 "annulus",
 338                 "female flowers",
 339                 "Male flowers",
 340                 "Female",
 341                 "Infructescences",    //order not consistent (sometimes before "Flowers")
 342                 "Fruit",
 343                 "Fruits",
 344                 "fruiting axes",
 345                 "drupes",
 346                 "Arillode",
 347                 "seed",
 348                 "Seeds",
 349                 "Seedling",
 350                 "flower tube",
 351                 "nutlets",
 352                 "pollen",
 353                 "secondary xylem",
 354                 "chromosome number",
 355
 356                 "figure",
 357                 "fig",
 358                 "figs",
 359
 360
 361
 362         };
 363
 364         public FeatureNode addFeataureNodesByStringList(String[] featureStringList, FeatureNode root, IInputTransformer transformer, ITermService termService){
 365                 FeatureNode lastChild = null;
 366                 try {
 367                         for (String featureString : featureStringList){
 368                                 UUID featureUuid;
 369                                 featureUuid = transformer.getFeatureUuid(featureString);
 370                                 Feature feature = (Feature)termService.find(featureUuid);
 371                                 if (feature != null){
 372                                         FeatureNode child = FeatureNode.NewInstance(feature);
 373                                         root.addChild(child);
 374                                 }
 375                         }
 376
 377                 } catch (UndefinedTransformerMethodException e) {
 378                         logger.error("getFeatureUuid is not implemented in transformer. Features could not be added");
 379                 }
 380                 return lastChild;
 381         }
 382
 383
 384
 385         /**
 386          * @param args
 387          */
 388         public static void main(String[] args) {
 389                 FloraMalesianaVol13Activator me = new FloraMalesianaVol13Activator();
 390                 me.doImport(cdmDestination);
 391         }
 392
 393 }